miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
17508	3'	-52.3	NC_004456.1	+	28905	0.66	0.774162
	Target:  5'- -cGCCCAg--CCCggcGUUCGAGCCAUu- -3' miRNA:   3'- uuUGGGUauaGGG---CGAGUUCGGUAcc -5'
17508	3'	-52.3	NC_004456.1	+	14032	0.66	0.774162
	Target:  5'- -cGCuCCAUggCUCGCUCAAGCggggcaAUGGc -3' miRNA:   3'- uuUG-GGUAuaGGGCGAGUUCGg-----UACC- -5'
17508	3'	-52.3	NC_004456.1	+	16065	0.66	0.752714
	Target:  5'- -uACCUGccUAUCCuugaCGCUCAAGCCG-GGu -3' miRNA:   3'- uuUGGGU--AUAGG----GCGAGUUCGGUaCC- -5'
17508	3'	-52.3	NC_004456.1	+	14543	0.66	0.752714
	Target:  5'- uGAGCCaagaCAUucAUCCCGCUUucGCCAcgcuUGGc -3' miRNA:   3'- -UUUGG----GUA--UAGGGCGAGuuCGGU----ACC- -5'
17508	3'	-52.3	NC_004456.1	+	36194	0.7	0.558902
	Target:  5'- gGAugCCAUGg-CCGCUCAGGCUGgccuUGGu -3' miRNA:   3'- -UUugGGUAUagGGCGAGUUCGGU----ACC- -5'
17508	3'	-52.3	NC_004456.1	+	28330	0.71	0.5031
	Target:  5'- -cGCCCAg--CCCggcGCUCGAGCCAUu- -3' miRNA:   3'- uuUGGGUauaGGG---CGAGUUCGGUAcc -5'
17508	3'	-52.3	NC_004456.1	+	13959	0.73	0.380891
	Target:  5'- ---gCCAUugcCCCGCUgagCGAGCCAUGGa -3' miRNA:   3'- uuugGGUAua-GGGCGA---GUUCGGUACC- -5'
17508	3'	-52.3	NC_004456.1	+	22696	1.09	0.001178
	Target:  5'- cAAACCCAUAUCCCGCUCAAGCCAUGGg -3' miRNA:   3'- -UUUGGGUAUAGGGCGAGUUCGGUACC- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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